+++ /dev/null
-<html>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
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- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Alignment Window Menus</title>
-</head>
-
-<body>
- <p>
- <strong>Alignment Window Edit Menu</strong>
- </p>
- <ul>
- <li><strong>Undo (Control Z)</strong><em><br> This
- will undo any edits you make to the alignment. This applies to
- insertion or deletion of gaps, cutting residues or sequences
- from the alignment or pasting sequences to the current alignment
- or sorting the alignment. <strong>NOTE:</strong> It DOES NOT
- undo colour changes, adjustments to group sizes, or changes to
- the annotation panel. </em></li>
- <li><strong>Redo (Control Y)<br>
- </strong><em>Any actions which you undo can be redone using redo. </em></li>
- <li><strong>Cut (Control X)<br>
- </strong><em>This will make a copy of the currently selected residues
- before removing them from your alignment. Click on a sequence
- name if you wish to select a whole sequence. <br> Use
- <CTRL> and X (<APPLE> and X on MacOSX) to cut.
- </em></li>
- <li><strong>Copy (Control C)</strong><br> <em>Copies
- the currently selected residues to the system clipboard - you
- can also do this by pressing <CTRL> and C (<APPLE>
- and C on MacOSX). <br> If you try to paste the clipboard
- contents to a text editor, you will see the format of the copied
- residues FASTA.
- </em></li>
- <li><strong>Paste </strong>
- <ul>
- <li><strong>To New Alignment (Control Shift V)<br>
- </strong><em>A new alignment window will be created from sequences
- previously copied or cut to the system clipboard. <br>
- Use <CTRL> and <SHIFT> and V(<APPLE> and
- <SHIFT;> and and V on MacOSX) to paste.
- </em></li>
- <li><strong>Add To This Alignment (Control V)<br>
- </strong><em>Copied sequences from another alignment window can be
- added to the current Jalview alignment. </em></li>
- </ul></li>
- <li><strong>Delete (Backspace)<br>
- </strong><em>This will delete the currently selected residues without
- copying them to the clipboard. Like the other edit operations,
- this can be undone with <strong>Undo</strong>.
- </em></li>
- <li><strong>Remove Left (Control L)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the left of the leftmost marked column. To mark a
- column, mouse click the scale bar above the alignment. Click
- again to unmark a column, or select "Deselect All" to
- deselect all columns.</em></li>
- <li><strong>Remove Right (Control R)<br>
- </strong><em>If the alignment has marked columns, the alignment will be
- trimmed to the right of the rightmost marked column. To mark a
- column, mouse click the scale bar above the alignment. Click
- again to unmark a column, or select "Deselect All" to
- deselect all columns.</em></li>
- <li><strong>Remove Empty Columns (Control E)<br>
- </strong><em>All columns which only contain gap characters
- ("-", ".") will be deleted.<br> You may
- set the default gap character in <a
- href="../features/preferences.html">preferences</a>.
- </em></li>
- <li><strong>Remove All Gaps (Control Shift E)</strong><br>
- <em>Gap characters ("-", ".") will be
- deleted from the selected area of the alignment. If no selection
- is made, ALL the gaps in the alignment will be removed.<br>
- You may set the default gap character in <a
- href="../features/preferences.html">preferences</a>.
- </em></li>
- <li><strong>Remove Redundancy (Control D)<br>
- </strong><em>Selecting this option brings up a window asking you to
- select a threshold. If the percentage identity between any two
- sequences (under the current alignment) exceeds this value then
- one of the sequences (the shorter) is discarded. Press the
- "Apply" button to remove redundant sequences. The
- "Undo" button will undo the last redundancy deletion.</em></li>
- <li><strong>Pad Gaps<br>
- </strong><em>When selected, the alignment will be kept at minimal width
- (so there are no empty columns before or after the first or last
- aligned residue) and all sequences will be padded with gap
- characters before and after their terminating residues.<br>
- This switch is useful when making a tree using unaligned
- sequences and when working with alignment analysis programs
- which require 'properly aligned sequences' to be all the same
- length.<br> You may set the default for <strong>Pad
- Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.
- </em></li>
- </ul>
-</body>
-</html>
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